6ZBO

HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6-morpholinopyrimidin-4-yl)-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-5-ol (Molidustat)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Prolyl Hydroxylase Domain Inhibition by Molidustat.

Figg Jr., W.D.McDonough, M.A.Chowdhury, R.Nakashima, Y.Zhang, Z.Holt-Martyn, J.P.Krajnc, A.Schofield, C.J.

(2021) ChemMedChem 16: 2082-2088

  • DOI: https://doi.org/10.1002/cmdc.202100133
  • Primary Citation of Related Structures:  
    6ZBN, 6ZBO

  • PubMed Abstract: 

    Human prolyl-hydroxylases (PHDs) are hypoxia-sensing 2-oxoglutarate (2OG) oxygenases, catalysis by which suppresses the transcription of hypoxia-inducible factor target genes. PHD inhibition enables the treatment of anaemia/ischaemia-related disease. The PHD inhibitor Molidustat is approved for the treatment of renal anaemia; it differs from other approved/late-stage PHD inhibitors in lacking a glycinamide side chain. The first reported crystal structures of Molidustat and IOX4 (a brain-penetrating derivative) complexed with PHD2 reveal how their contiguous triazole, pyrazolone and pyrimidine/pyridine rings bind at the active site. The inhibitors bind to the active-site metal in a bidentate manner through their pyrazolone and pyrimidine nitrogens, with the triazole π-π-stacking with Tyr303 in the 2OG binding pocket. Comparison of the new structures with other PHD inhibitor complexes reveals differences in the conformations of Tyr303, Tyr310, and a mobile loop linking β2-β3, which are involved in dynamic substrate binding/product release.


  • Organizational Affiliation

    Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Egl nine homolog 1
A, B, C, D, E
A, B, C, D, E, F
227Homo sapiensMutation(s): 0 
Gene Names: EGLN1C1orf12PNAS-118PNAS-137
EC: 1.14.11.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT9 (Homo sapiens)
Explore Q9GZT9 
Go to UniProtKB:  Q9GZT9
PHAROS:  Q9GZT9
GTEx:  ENSG00000135766 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZT9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QEQ (Subject of Investigation/LOI)
Query on QEQ

Download Ideal Coordinates CCD File 
BA [auth F]
H [auth A]
M [auth B]
Q [auth C]
T [auth D]
BA [auth F],
H [auth A],
M [auth B],
Q [auth C],
T [auth D],
X [auth E]
2-(6-morpholin-4-ylpyrimidin-4-yl)-4-(1,2,3-triazol-1-yl)pyrazol-3-ol
C13 H14 N8 O2
NTIRTFLRBFAPSX-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
L [auth B]
P [auth C]
S [auth D]
AA [auth F],
G [auth A],
L [auth B],
P [auth C],
S [auth D],
W [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth F]
EA [auth F]
I [auth A]
J [auth A]
CA [auth F],
DA [auth F],
EA [auth F],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
R [auth C],
U [auth D],
V [auth D],
Y [auth E],
Z [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.119α = 90
b = 75.151β = 95.31
c = 127.215γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing
Cootmodel building
MolProbitymodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--
Cancer Research UKUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2021-12-08
    Changes: Data collection
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description